IRES Track I: US-Sweden Clinical Bioinformatics Research Training Program

IRES Track I：美国-瑞典临床生物信息学研究培训项目

• 批准号: 1951792
• 负责人: Mark Chapman
• 金额: $ 29.92万
• 依托单位: University of San Diego
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-09-01 至 2024-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1951792&HistoricalAwards=false
• 关键词: IRES; Track; US; Sweden; Clinical

The publication of the first human genome in 2001 transformed biomedical research. Since then, an explosion of new technologies has required engineers and computer scientists to invent computational methods to analyze and interpret complex biological datasets. The efforts to develop these computational methods created the new field of bioinformatics. Over the past two decades, bioinformatics methods have aided in the development of diagnostics, therapies, and predictive models of many disease, including cancer, diabetes, and heart disease. The continual development of bioinformatics tools to analyze and interpret biological data is critical to advancing data-driven healthcare. Therefore, the future of healthcare depends on developing educational programs to train young scientists as bioinformaticians. Given this need, this IRES site aims to train 6 undergraduate students per year from primarily undergraduate institutions (PUIs) in Southern California to conduct 10 weeks of supervised bioinformatics research at the Science for Life Laboratory (SciLifeLab) in Stockholm, Sweden. SciLifeLab is a consortium of researchers from Sweden’s top universities: the Karolinska Institute, Stockholm University, The Royal Institute of Technology, and Uppsala University, and is a global leader in using genomic data and bioinformatics to advance human health. In addition to educating the next generation of bioinformaticians, a goal of this program is to train a diverse cohort of researchers that become globally-engaged scientists. To achieve this, this IRES program will focus on recruiting students from PUIs who are traditionally under-represented in engineering. Recruitment will focus on PUIs because these students typically have fewer research opportunities at their home institutions and will greatly benefit from this program. To ensure student success, extensive predeparture training will provide a foundation in bioinformatics and prepare students for living abroad. Furthermore, upon returning from Sweden, students will have the opportunity to present their work at the annual Biomedical Engineering Society meeting and will be encouraged to maintain an active virtual collaboration with their research group at SciLifeLab. The diverse array of projects which the IRES students will be involved in are at the forefront of clinical bioinformatics. Specifically, students will be involved in developing computational methods to better understand kidney, breast and liver cancers, abdominal aortic aneurysms, skeletal muscle adaptation to exercise and the spatial organization of chromosomes in the nucleus. All of these projects involve analyzing sequencing data from clinically relevant (i.e. human) samples to broaden our knowledge of fundamental biology and the diagnosis/treatment of human disease. Additionally, this work advances engineering knowledge by developing new computational methods useful to the field of bioinformatics. Not only does this program seek to provide exciting research opportunities for undergraduate students, but it also gives these students a chance to live abroad and experience a different culture. Exposure to different cultural backgrounds and ways of thinking can influence student global perspectives and challenge preconceived notions about the world. Moreover, working with researchers from different cultural backgrounds will give students tools to communicate in our ever-globalizing society. This program will likely be the first time abroad for many of the student participants, so the experience will be both professionally and personally formative.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

2001年第一个人类基因组的发表改变了生物医学研究。从那时起，新技术的爆炸式发展要求工程师和计算机科学家发明计算方法来分析和解释复杂的生物数据集。开发这些计算方法的努力创造了生物信息学的新领域。在过去的二十年里，生物信息学方法已经帮助开发了许多疾病的诊断，治疗和预测模型，包括癌症，糖尿病和心脏病。生物信息学工具的不断发展，以分析和解释生物数据是推进数据驱动的医疗保健的关键。因此，医疗保健的未来取决于开发教育计划，将年轻科学家培养为生物信息学家。鉴于这一需求，这个IRES网站的目标是每年培训6名本科生，主要来自南加州的本科院校（PUI），在瑞典斯德哥尔摩的生命科学实验室（SciLifeLab）进行为期10周的监督生物信息学研究。SciLifeLab是由来自瑞典顶尖大学的研究人员组成的联盟：卡罗林斯卡学院，斯德哥尔摩大学，皇家理工学院和乌普萨拉大学，是利用基因组数据和生物信息学促进人类健康的全球领导者。除了教育下一代生物信息学家，该计划的目标是培养一批多样化的研究人员，成为全球参与的科学家。为了实现这一目标，该IRES计划将专注于从传统上在工程领域代表性不足的PUI招募学生。招聘将集中在PUI，因为这些学生通常在他们的家乡机构有较少的研究机会，并将大大受益于这一计划。为了确保学生的成功，广泛的出发前培训将提供生物信息学的基础，并为学生在国外生活做好准备。此外，从瑞典返回后，学生将有机会在生物医学工程学会年会上展示他们的工作，并鼓励他们与SciLifeLab的研究小组保持积极的虚拟合作。IRES学生将参与的各种项目处于临床生物信息学的最前沿。具体而言，学生将参与开发计算方法，以更好地了解肾癌，乳腺癌和肝癌，腹主动脉瘤，骨骼肌对运动的适应以及细胞核中染色体的空间组织。所有这些项目都涉及分析临床相关（即人类）样本的测序数据，以拓宽我们对基础生物学和人类疾病诊断/治疗的知识。此外，这项工作通过开发对生物信息学领域有用的新计算方法来推进工程知识。该计划不仅旨在为本科生提供令人兴奋的研究机会，而且还为这些学生提供了在国外生活和体验不同文化的机会。接触不同的文化背景和思维方式可以影响学生的全球视野，并挑战对世界的先入为主的观念。此外，与来自不同文化背景的研究人员合作将为学生提供在我们日益全球化的社会中进行交流的工具。这个项目对许多学生来说可能是第一次出国，所以这段经历将对他们的专业和个人成长都有很大的影响。这个奖项反映了NSF的法定使命，并通过使用基金会的智力价值和更广泛的影响审查标准进行评估，被认为是值得支持的。

项目成果

US-Sweden Bioinformatics NSF-IRES Year 1: Program Development and Initial Lessons Learned

美国-瑞典生物信息学 NSF-IRES 第一年：项目开发和初步经验教训

• 发表时间: 2022
• 期刊: 2022 American Society for Engineering Education Annual Conference and Exposition
• 作者: Chapman, Mark A

US-Sweden Bioinformatics IRES: Investigating Engineering Students’ Attitudes and Perspectives Throughout a 10-week International Research Program

美国-瑞典生物信息学 IRES：在为期 10 周的国际研究项目中调查工程专业学生的态度和观点

• 发表时间: 2022
• 期刊: 2022 American Society for Engineering Education Annual Conference & Exposition
• 作者: Chapman, Mark A;Forbes, Marissa H.
• 通讯作者: Forbes, Marissa H.

Work in Progress: Development of a Training Program to Prepare Students for an Immersive Bioinformatics Summer Research Experience

正在进行的工作：制定培训计划，为学生提供沉浸式生物信息学夏季研究体验

• 发表时间: 2021
• 期刊: 2021 American Society for Engineering Education Virtual Annual Conference
• 作者: Chapman, MA

Discovery of drug targets and therapeutic agents based on drug repositioning to treat lung adenocarcinoma

• DOI: 10.1016/j.biopha.2023.114486
• 发表时间: 2023-03-10
• 期刊: BIOMEDICINE & PHARMACOTHERAPY
• 影响因子: 7.5
• 作者: Graves, Occam Kelly;Kim, Woonghee;Li, Xiangyu
• 通讯作者: Li, Xiangyu

US-Sweden Bioinformatics IRES Year 2: Improving Student Preparedness

美国-瑞典生物信息学 IRES 第 2 年：提高学生的准备程度

• 发表时间: 2023
• 期刊: 2023 ASEE Annual Conference & Exposition
• 作者: Chapman, Mark A.